Contacts of the helix formed by residues 263 - 279 (chain A) in PDB entry 3L6D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLU* 3.4 24.5 - - + -
196A ALA* 4.3 10.1 - - + -
256A LEU* 3.7 32.5 - - + +
257A HIS* 4.8 3.4 + - - -
261A VAL* 3.6 25.0 + - + -
262A TRP* 1.3 81.3 - - - +
264A PRO* 1.3 61.7 - - - +
265A VAL 3.1 3.0 + - - -
266A PHE* 3.2 8.0 + - + +
267A ASP* 2.8 41.2 + - - -
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Residues in contact with PRO 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU* 3.1 6.1 - - - +
262A TRP* 3.4 46.7 - - + +
263A THR* 1.3 88.0 - - - +
265A VAL* 1.3 54.3 + - - +
267A ASP* 3.4 13.3 - - + +
268A ALA* 3.0 22.0 + - - +
268B ALA* 3.5 14.5 - - + +
271B GLN* 4.2 13.9 - - - +
272B VAL* 3.4 30.3 - - + -
293B PHE* 4.3 1.6 - - + -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 4.1 10.3 - - + +
189A THR* 3.8 25.8 - - + -
192A GLU* 2.8 28.8 + - + +
264A PRO* 1.3 68.1 - - - +
266A PHE* 1.3 66.2 + - - +
268A ALA* 3.1 5.0 + - - +
269A VAL* 2.9 23.0 + - + +
185B ALA* 5.0 0.7 - - + -
265B VAL* 3.6 26.0 - - + +
268B ALA* 3.9 7.9 - - - -
269B VAL* 3.8 36.6 - - + +
272B VAL* 4.1 10.1 - - + -
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLU* 2.8 20.7 + - - +
249A PHE* 3.5 23.6 - + + -
252A ILE* 3.5 31.2 - - + -
253A ALA* 3.9 7.2 - - + -
256A LEU* 4.0 16.6 - - + -
263A THR* 3.2 11.9 + - + +
265A VAL* 1.3 73.8 - - - +
267A ASP* 1.3 57.8 + - - +
269A VAL* 3.1 18.6 + - + +
270A CYS* 2.9 50.3 + - - -
180B HIS 4.5 0.2 - - - -
181B ALA* 3.5 42.6 - - + -
184B PHE* 4.4 11.0 - - + -
185B ALA* 4.2 8.5 - - + +
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Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA* 5.1 4.7 - - - +
257A HIS* 2.8 37.4 + - - -
262A TRP* 5.5 4.2 + - - -
263A THR* 2.8 32.2 + - - +
264A PRO* 3.4 13.7 - - + +
266A PHE* 1.3 71.6 - - - +
268A ALA* 1.3 56.4 + - - +
270A CYS* 3.3 10.5 + - - +
271A GLN* 3.0 25.6 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PRO 3.0 11.3 + - - +
265A VAL 3.4 8.1 - - - +
267A ASP* 1.3 75.6 - - - +
269A VAL* 1.3 60.7 + - - +
271A GLN* 3.2 14.5 + - - +
272A VAL* 3.0 32.1 + - - +
264B PRO* 3.6 30.1 - - + +
265B VAL* 3.8 13.2 - - - -
268B ALA* 4.0 4.5 - - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 3.7 18.2 - - + -
265A VAL 2.9 18.0 + - - +
266A PHE* 3.3 17.7 - - + +
268A ALA* 1.3 74.6 - - - +
270A CYS* 1.3 62.1 + - - +
272A VAL* 3.2 4.3 + - - +
273A VAL* 3.1 21.7 + - - +
184B PHE 4.4 0.2 - - - +
185B ALA* 3.7 34.8 - - + -
188B VAL* 3.6 31.9 - - + -
265B VAL* 4.1 24.0 - - + -
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Residues in contact with CYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PHE* 3.8 29.8 - - + -
250A ALA* 4.8 1.3 - - - -
253A ALA* 4.0 12.1 - - + -
266A PHE* 2.9 45.8 + - - -
267A ASP* 3.4 11.4 - - - +
269A VAL* 1.3 76.7 - - - +
271A GLN* 1.3 52.1 + - - +
273A VAL* 3.4 1.8 + - - +
274A GLN* 2.7 51.9 + - - +
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ASP 3.0 13.2 + - - +
268A ALA* 3.2 11.7 + - - +
270A CYS* 1.3 76.3 - - - +
272A VAL* 1.3 61.1 + - - +
274A GLN* 3.7 7.6 + - - +
275A ARG* 3.2 29.6 + - + +
262B TRP* 4.3 21.5 - - + +
264B PRO* 3.8 19.8 - - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA 3.0 17.5 + - - +
269A VAL 3.5 8.1 - - - +
271A GLN* 1.3 73.0 - - - +
273A VAL* 1.3 60.2 + - - +
275A ARG* 3.3 5.5 - - - +
276A ALA* 3.0 25.5 + - - +
289A THR* 3.6 22.2 - - + -
292A SER* 4.6 4.9 + - - +
293A PHE* 3.5 31.6 - - + -
188B VAL* 4.0 10.1 - - + -
262B TRP* 4.2 10.7 - - + -
264B PRO* 3.5 27.6 - - + -
265B VAL* 3.9 12.3 - - + -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.5 16.3 - - + +
245A HIS 4.5 0.7 - - - -
246A ALA* 3.8 34.3 - - + +
249A PHE* 3.5 32.1 - - + -
269A VAL 3.1 11.4 + - - +
270A CYS 4.0 2.7 - - - +
272A VAL* 1.3 76.7 - - + +
274A GLN* 1.3 65.9 + - - +
276A ALA* 3.2 8.7 + - - +
277A ALA* 2.9 19.1 + - - +
286A ILE* 4.5 6.5 - - + -
289A THR* 4.4 13.0 - - - +
188B VAL* 4.0 14.8 - - + -
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ALA* 4.1 20.5 + - - +
249A PHE* 6.0 0.4 - - - +
250A ALA* 4.6 19.0 - - - +
270A CYS* 2.7 43.4 + - - +
271A GLN* 3.9 7.0 - - - +
273A VAL* 1.3 75.0 - - - +
275A ARG* 1.3 52.9 - - + +
277A ALA* 3.1 10.3 + - - +
278A ALA* 2.8 34.2 + - - +
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLN* 3.2 18.0 + - + +
272A VAL 3.3 10.5 - - - +
274A GLN* 1.3 77.9 - - + +
276A ALA* 1.3 59.5 + - - +
278A ALA* 3.0 11.4 + - + +
279A MSE 2.8 72.6 + - - +
292A SER* 3.7 11.6 + - - +
262B TRP* 3.6 43.6 - - + -
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LEU* 3.9 22.9 - - + -
272A VAL 3.0 13.5 + - - +
273A VAL* 3.2 10.7 + - - +
275A ARG* 1.3 74.5 - - - +
277A ALA* 1.3 63.1 + - - +
279A MSE 3.3 6.0 + - - -
280A GLY 3.4 0.2 + - - -
281A TYR* 3.1 39.4 + - + +
289A THR* 4.6 7.2 - - - +
292A SER* 4.2 21.0 - - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.7 13.5 - - + +
243A ASP* 5.4 4.5 - - + -
246A ALA* 4.8 11.2 - - + -
273A VAL 2.9 12.4 + - - +
274A GLN* 3.3 12.1 - - - +
276A ALA* 1.3 75.8 - - - +
278A ALA* 1.3 62.4 + - - +
280A GLY* 3.1 14.4 + - - -
281A TYR 4.2 0.2 + - - -
282A GLY* 4.2 14.2 + - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A GLN 2.8 16.9 + - - +
275A ARG* 3.0 14.1 + - + +
277A ALA* 1.3 73.4 - - - +
279A MSE 1.3 58.7 + - + +
280A GLY* 3.1 3.9 + - - -
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Residues in contact with MSE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ARG* 2.8 58.6 + - - +
276A ALA 3.7 5.8 - - - +
277A ALA 3.2 0.4 - - - -
278A ALA* 1.3 76.8 - - + +
280A GLY* 1.3 58.9 + - - +
281A TYR* 3.5 18.5 - - + -
292A SER* 3.8 36.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il